Marvinbeans (v. 5.8.2) error on structure containing R-Group

User 672cb907e4

29-02-2012 17:32:50


To Whom It May Concern,


I have been using marvinbeans for calculating masses and formula or structure using MDL molfile.  However, I have encountered a problem if the structure contains R-Group in the molfile.


For example, using the cxcalc (I tested both Ver. 5.6.0 and Ver. 5.8.2) to calculate the mass and formula of a structure "Fatty Acid".


It returns me as follows


/marvinbeans/cxcalc LMFA01010000.mol formula


id Formula


1 C2H4O2


 


/marvinbeans/cxcalc LMFA01010000.mol exactmass


id Exact mass


1 60.021129372


 


/marvinbeans/cxcalc LMFA01010000.mol formalcharge


id Formal charge


1 0


 


I believe it should return me NULL, NOTHING, or CHO2R for formula, and NULL for exactmass


 


Please feel free to use the attached mol file for your reference, and let me know if there are any solutions to fix this problem.  Since I need to filter out the ones that have R-group in our structure db.


 


Thank you in advance for your support.


 


Best Regards,


Kevin


ChemAxon 5433b8e56b

02-03-2012 13:57:28

Hi Kevin,


i have moved your message to the Calculations related forum topic, my colleagues will answer for you soon.


Thank you for your patience.


Regards,
Istvan

ChemAxon e08c317633

02-03-2012 16:12:56

Kevin, you are right, it is how calculations work if the molecule contains real R-groups. Pleas note, that the atom marked with "R" in your molecule is not a real R-group, but a carbon atom with an "R" alias.


The .mol source of the attached molecule:


LMFA01010000 
LIPDMAPS01251212252D

4 3 0 0 0 0 0 0 0 0999 V2000
6.4291 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.7145 5.4114 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7145 6.2374 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.0000 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
2 4 1 0 0 0 0
A 4
R
M END
> <LM_ID>
LMFA01010000

> <COMMON_NAME>
fatty acid

> <SYSTEMATIC_NAME>
fatty acid

> <CATEGORY>
Fatty Acyls [FA]

> <MAIN_CLASS>
Fatty Acids and Conjugates [FA01]

> <SUB_CLASS>
Straight chain fatty acids [FA0101]

> <PUBCHEM_SID>
24701115

> <KEGG_ID>
C00162

> <HMDBID>
HMDB00142

> <CHEBI_ID>
15740

> <LIPID_MAPS_CMPD_URL>
http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA01010000

> <PUBCHEM_SUBSTANCE_URL>
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=24701115

$$$$

The atoms in the molecule: O, C, O, C


You can use Structure Checker to find such kind of errors.


Zsolt